I'm going to change power source from the usb cable to plugging in a 9v battery to the positive/negative pinholes on my breadboard. Will I fry my board with a 9v battery? I know most of the examples run on 5v, how will I be affected?
Will I fry my board with a 9v battery?
Yes.
even with terminals pos to pos AND neg to neg? What can I do to avoid frying my board and yet run my aduino board/breadboard combo independently? 
Get a voltage regulator to cut down the 9V to 5V.